sim.hotspot: Wrapper routine for simulations.

In qtlhot: Inference for QTL Hotspots

Description

Wrapper routine for simulations

Usage

sim.hotspot(nSim, cross, n.pheno, latent.eff, res.var = 1, n.quant, n.perm,
  alpha.levels, lod.thrs, drop.lod = 1.5, verbose = FALSE)
mySimulations(...)
sim.null.cross(chr.len = rep(400, 16), n.mar = 185, n.ind = 112,
  type = "bc", n.pheno = 6000, latent.eff = 1.5, res.var = 1,
  init.seed = 92387475)
sim.null.pheno.data(cross, n.pheno, latent.eff, res.var)
include.hotspots(cross, hchr, hpos, hsize, Q.eff, latent.eff,
  lod.range.1, lod.range.2, lod.range.3, res.var=1, n.pheno, init.seed)

Arguments

nSim	Number of simulated sets of phenotypes to create. See details.
cross	Object of class cross. See read.cross.
n.pheno	Number of traits, or phenotypes, to simulate for cross object.
latent.eff	Strength of latent effect, which is included in all traits. See sim.null.cross.
res.var	Residual variance for traits. Should not affect results.
n.quant	maximum size of hotspots examined; ideally large enough to exceed the largest Breitling alpha critical value.
n.perm	Number of permutations to perform per realization. Good idea to do 1000, but this takes time.
alpha.levels	Vector of significance levels.
lod.thrs	Vector of LOD thresholds, typically single-trait permutation thresholds for various significance levels.
drop.lod	Drop in LOD score examined. LODs below this drop from the maximum for a chromosome will not be scored.
init.seed	initial seed for pseudo-random number generation
chr.len	vector of chromosome lengths
n.mar	number of markers
n.ind	number of individuals
type	type of cross
hchr,hpos,hsize	vectors for hotspot chromosomes, positions, and sizes
Q.eff	QTL effect
lod.range.1,lod.range.2,lod.range.3	2-vectors of LOD ranges for multiple purposes
verbose	Verbose output if TRUE. More detailed output if 2.
...	Arguments passed directly to sim.hotspot.

Details

Simulate nSim realizations of cross object with n.pheno phenotypes with correlation latent.eff. All simulations use the same genotypes in the cross object.

Value

sim.null.cross simulates an object of class cross. sim.null.pheno.data simulates a data frame of phenotypes. sim.hotspot uses these other routines to simulate a hotspot, returning an list object.

Author(s)

Elias Chaibub Neto and Brian S. Yandell

See Also

sim.null.cross, read.cross.

Examples

ncross1 <- sim.null.cross(chr.len = rep(100, 4),
                          n.mar = 51,
                          n.ind = 100,
                          type = "bc",
                          n.phe = 1000,
                          latent.eff = 3,
                          res.var = 1,
                          init.seed = 123457)
cross1 <- include.hotspots(cross = ncross1,
                           hchr = c(2, 3, 4),
                           hpos = c(25, 75, 50),
                           hsize = c(100, 50, 20),
                           Q.eff = 2,
                           latent.eff = 3,
                           lod.range.1 = c(2.5, 2.5),
                           lod.range.2 = c(5, 8),
                           lod.range.3 = c(10, 15),
                           res.var = 1,
                           n.phe = 1000,
                           init.seed = 12345)

Example output

Loading required package: qtl
Loading required package: lattice
Loading required package: corpcor
Loading required package: mnormt

qtlhot documentation built on May 2, 2019, 11:06 a.m.